1 Mount Hood Environmental, PO Box 1303, Challis, Idaho, 83226, USA
2 Mount Hood Environmental, 39085 Pioneer Boulevard #100 Mezzanine, Sandy, Oregon, 97055, USA
3 Mount Hood Environmental, PO Box 4282, McCall, Idaho, 83638, USA

✉ Correspondence: Bryce N. Oldemeyer <>, Mark Roes <>

1 Background

This is the skeleton rmd outlining the development of a revised (“new”) QRF model (See et al. 2021). This will eventually highlight the covariate selection process, QRF model fit, the RF extrapolation model, and finally compare extrapolation estimates between the original and new models for eight watersheds within the Upper Salmon Basin.

1.1 Covariate selection

Explain covariate selection process. DASH/resto compatible, high MIC, low correlation, missing data, lots of zeros, species specific models, and eventually converting to joint models.

1.2 QRF Model fit

Talk about relative importance and pdp plots.

1.3 Extrapolation model

Talk about GAA’s

1.4 Extrapolation comparison

Extrapolations of habitat capacity for Chinook salmon, by life-stage, within the North Fork Salmon watershed.

Figure 1.1: Extrapolations of habitat capacity for Chinook salmon, by life-stage, within the North Fork Salmon watershed.

Extrapolations of habitat capacity for steelhead, by life-stage, within the North Fork Salmon watershed..

Figure 1.2: Extrapolations of habitat capacity for steelhead, by life-stage, within the North Fork Salmon watershed..

1.5 QRF Habitat Capacity Estimates

1.5.0.1 Chinook Salmon

Table 1.1: Predicted Chinook salmon habitat capacity by life-stage and watershed.
Watershed Juv summer capacity Summer SE Juv winter capacity Winter SE Redd capacity Redd SE
EF Salmon 1,926,623 226,925.7 0 24,264 402 21
Lemhi 786,452 62,659.8 2,097 10,576 353 11
NF Salmon 339,275 50,147.9 69,653 10,156 166 8
Pahsimeroi 265,099 18,409.2 87,150 9,740 139 4
Panther Cr 1,219,542 118,369.5 197,732 21,729 448 17
Upper Salmon 3,301,286 352,419.5 0 28,116 575 29
Valley Cr 1,902,198 207,362.9 0 16,913 394 20
Yankee Fork 2,144,056 274,555.8 86 23,615 438 23

1.5.0.2 Steelhead

Table 1.2: Predicted winter steelhead habitat capacity by watershed.
Watershed Juv summer capacity Summer SE Juv winter capacity Winter SE Redd capacity Redd SE
EF Salmon 252,597 15,520.5 19,034 19,766 413 24
Lemhi 310,577 9,082.3 44,384 13,200 441 18
NF Salmon 242,471 18,381.8 308,117 27,964 323 22
Pahsimeroi 159,705 6,225.1 205,427 13,825 198 8
Panther Cr 268,476 13,598.0 340,427 20,084 317 15
Upper Salmon 243,548 14,843.6 11,920 22,796 452 32
Valley Cr 176,048 10,707.6 17,219 16,914 365 26
Yankee Fork 197,926 12,378.9 5,427 22,159 449 36

1.5.1 Comparison with previous extrapolation

We have generated

Predicted change in Chinook salmon habitat capacity compared to the previous extrapolation, by life-stage, within the North Fork Salmon watershed.

Figure 1.3: Predicted change in Chinook salmon habitat capacity compared to the previous extrapolation, by life-stage, within the North Fork Salmon watershed.

Table 1.3: Estimated chinook capacities and comparison with previous random forest extrapolations for eight watersheds
Model Watershed Predicted capacity Capacity % change Predicted capacity SE SE % change
Juv summer EF Salmon 1,926,623.4 112 226,926 186
Juv summer Lemhi 786,451.7 112 62,660 172
Juv summer NF Salmon 339,275.4 13 50,148 100
Juv summer Pahsimeroi 265,099.3 45 18,409 54
Juv summer Panther Cr 1,219,541.6 21 118,369 33
Juv summer Upper Salmon 3,301,286.0 163 352,419 205
Juv summer Valley Cr 1,902,197.5 152 207,363 191
Juv summer Yankee Fork 2,144,056.4 222 274,556 284
Juv winter EF Salmon 0.0 -100 24,264 76
Juv winter Lemhi 2,096.6 -99 10,576 57
Juv winter NF Salmon 69,652.8 26 10,156 101
Juv winter Pahsimeroi 87,150.1 -8 9,740 44
Juv winter Panther Cr 197,731.8 27 21,729 116
Juv winter Upper Salmon 0.0 -100 28,116 15
Juv winter Valley Cr 0.0 -100 16,913 27
Juv winter Yankee Fork 86.1 -100 23,615 83
Redds EF Salmon 401.9 -13 21 -29
Redds Lemhi 353.0 5 11 19
Redds NF Salmon 165.7 -5 8 -4
Redds Pahsimeroi 139.4 25 4 17
Redds Panther Cr 447.8 -4 17 -14
Redds Upper Salmon 575.0 -20 29 -41
Redds Valley Cr 393.7 -29 20 -44
Redds Yankee Fork 438.2 -38 23 -59

1.5.1.1 Steelhead

Predicted change in winter steelhead habitat capacity compared to the previous extrapolation, by life-stage, within the North Fork Salmon watershed.

Figure 1.4: Predicted change in winter steelhead habitat capacity compared to the previous extrapolation, by life-stage, within the North Fork Salmon watershed.

Table 1.4: Estimated winter steelhead capacities and comparison with previous random forest extrapolations for eight watersheds
Model Watershed Predicted capacity Capacity % change Predicted capacity SE SE % change
Juv summer EF Salmon 252,597.2 -31 15,521 -1
Juv summer Lemhi 310,577.2 -15 9,082 11
Juv summer NF Salmon 242,471.4 -5 18,382 34
Juv summer Pahsimeroi 159,705.1 -18 6,225 14
Juv summer Panther Cr 268,475.9 -8 13,598 42
Juv summer Upper Salmon 243,548.0 -31 14,844 -11
Juv summer Valley Cr 176,047.8 -28 10,708 -11
Juv summer Yankee Fork 197,926.3 -29 12,379 38
Juv winter EF Salmon 19,033.8 -95 19,766 -30
Juv winter Lemhi 44,384.0 -89 13,200 -27
Juv winter NF Salmon 308,116.9 -2 27,964 4
Juv winter Pahsimeroi 205,426.6 -5 13,825 20
Juv winter Panther Cr 340,427.0 8 20,084 26
Juv winter Upper Salmon 11,920.1 -97 22,796 -30
Juv winter Valley Cr 17,219.1 -95 16,914 -40
Juv winter Yankee Fork 5,427.4 -99 22,159 -46
Redds EF Salmon 413.2 -13 24 -13
Redds Lemhi 441.4 10 18 12
Redds NF Salmon 323.4 -10 22 22
Redds Pahsimeroi 198.5 2 8 -8
Redds Panther Cr 317.0 -7 15 15
Redds Upper Salmon 452.1 -11 32 -6
Redds Valley Cr 365.0 -20 26 -7
Redds Yankee Fork 448.9 -25 36 13

1.5.2 Capacity by stream

1.5.2.1 Chinook

1.5.2.2 Steelhead